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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/nanosv">Debian Med / nanosv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanosv/-/commit/48726de432aeaa45818a19e5694073212f573a54">48726de4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-29T21:08:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Since toy.sam is available in the samtools package already, simply take the relevant file from there
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/nanosv/-/commit/3c875e1743e9caad42658d87e9ad88ac6a2e3ee9">3c875e17</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-29T21:10:39+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add recommends on sambamba
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/nanosv/-/commit/ace8e1103ee955bd8002e22c6275f3ae77d05286">ace8e110</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-05-29T21:10:43+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update Interim changelog entry
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="deleted-file">
−
debian/examples
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<a href="#bdfc46c0374a699b0769b0d4b52f7b32500402bf">
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−
debian/tests/data/read.sam
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,3 @@ in order to confirm its integrity.</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"></span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">files</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">testing</span> </span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span></pre>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Files</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">/*</span></span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Source</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">https</span><span class="o" style="font-weight: 600;">://</span><span class="n" style="color: #333;">github</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">com</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">samtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">samtools</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">blob</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">develop</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">examples</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">toy</span><span class="mf" style="color: #099;">.</span><span class="n" style="color: #333;">sam</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="php"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="php"></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">nanosv (1.2.4+git20190409.c1ae30c-4) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * <span class="idiff left right">Add test data</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * <span class="idiff left right">Team Upload.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> * Add examples and docs</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Wed, 26 May 2021 17:09:51 +0530</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +18,7 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: nanosv</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Recommends: sambamba</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> python3-pysam,</span>
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<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,10 +10,6 @@ Files: debian/*</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Copyright: 2020 Steffen Moeller <moeller@debian.org></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Files: debian/tests/data/*</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Copyright: 2008-2020 Genome Research Ltd.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">License : MIT</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> copy of this software and associated documentation files (the "Software"),</span>
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<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#bdfc46c0374a699b0769b0d4b52f7b32500402bf"><strong>debian/tests/data/read.sam</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@SQ SN:ref LN:45</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">@SQ SN:ref2 LN:40</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA *</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">r003 0 ref 9 30 5H6M * 0 0 AGCTAA *</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC *</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">r003 16 ref 29 30 6H5M * 0 0 TAGGC *</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">x1 0 ref2 1 30 20M * 0 0 aggttttataaaacaaataa ????????????????????</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">x2 0 ref2 2 30 21M * 0 0 ggttttataaaacaaataatt ?????????????????????</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">x3 0 ref2 6 30 9M4I13M * 0 0 ttataaaacAAATaattaagtctaca ??????????????????????????</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">x4 0 ref2 10 30 25M * 0 0 CaaaTaattaagtctacagagcaac ?????????????????????????</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">x5 0 ref2 12 30 24M * 0 0 aaTaattaagtctacagagcaact ????????????????????????</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">x6 0 ref2 14 30 23M * 0 0 Taattaagtctacagagcaacta ???????????????????????</span></pre>
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<a href="https://salsa.debian.org/med-team/nanosv/-/compare/a0c6fe0a2d2402755e55659a12e88a885771b908...ace8e1103ee955bd8002e22c6275f3ae77d05286#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,7 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>nanosv</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">examplepkg</span><span class="o" style="font-weight: 600;">=</span>samtools</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,18 +10,17 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;"><span class="idiff left right">*</span></span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;"><span class="idiff left">example</span>pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="idiff right">toy.sam</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> <span class="nt" style="color: #000080;">-f</span> toy.sam read.sam</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>read.sam| samtools view <span class="nt" style="color: #000080;">-Sb</span> <span class="o" style="font-weight: 600;">></span> reads.bam</span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell">samtools <span class="nb" style="color: #0086b3;">sort </span>reads.bam <span class="o" style="font-weight: 600;">></span> reads_sort.bam</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">samtools index reads_sort.bam reads_sort.bai</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell">bedtools bamtobed <span class="nt" style="color: #000080;">-i</span> reads_sort.bam <span class="o" style="font-weight: 600;">></span> target.bed</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">NanoSV reads_sort.bam <span class="nt" style="color: #000080;">-b</span> target.bed <span class="nt" style="color: #000080;">-s</span> sambamba <span class="nt" style="color: #000080;">-o</span> output.vcf </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"output.vcf"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS Test"</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Output generated is not consistent and cannot be compared with a reference. </span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"> </span></pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">NanoSV reads_sort.bam <span class="nt" style="color: #000080;">-b</span> target.bed <span class="nt" style="color: #000080;">-s</span> sambamba <span class="nt" style="color: #000080;">-o</span> output.vcf</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"output.vcf"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS Test"</span></span></pre>
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